I've tried a lot of things here and I can get them in by joining using the join waypoint but they need to go different ways when they land. [Array]grpNull works, but then squad 2 just stand around and stare at each other. I basically don't know what to do with them once they land.
There are some helpful tutorials but they don't seem to cover this all the way through. Any help would be most welcome aa I know little about init. scripts.

You should be able to get two groups into the chopper by just using the standard get in waypoints that way you can just carry on using separate waypoints after they get out.

You can also copy waypoints from one Group to another, to do that you need to place a unit at the unload position and give him some waypoints, Untick all boxes in the special state menus and give him a group name in Composition editor ie Gatekeeper.
Also name the Group getting out of the vehicle ie Pathfinder

Thanks, I'll give the second option a shot but using getin waypoints always resulted in the chopper taking off after the first group boarded and the second group headed off to their next waypoint on foot, which amusingly resulted in the commander swimming across the ocean with the rest of the group standing on the beach watching him swim off to certain death.
I'll let you know.

I tried a more simple version with no mods using get in and load but it is only ever one group that will board a helicopter; the other run off into the distance.
The copying waypoints changed the names of the AI's in 'Pathfinder' to nothing and they do stay at the landing site but don't follow 'Gatekeepers' waypoints. They just stand around watching the other guys heading off to war. I put the name in the comp edit variable name and the instruction in the Transport Unload 'on activation'.
There has to be a way to do this and it must have been done before by someone. Getting out of a chopper and heading in separate directions is not a new thing.
Any other possibilities?

I had a 'load' waypoint synced to the 'Get In' and' 'Get Out' synced to unload transport. I just snapped the 'Get in' WP's to the Helicopter and synced to the first 'Move' as in your example.
Couldn't be simpler. Thanks a lot for the sqm, it's made my week!